AMBER Archive (2009)

Subject: RE: [AMBER] Exclamation marks in trajectory

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jul 13 2009 - 13:13:17 CDT

Hi Hugh,

> I recently had a trajectory generated by PMEMD 10 that would only
> partially load in VMD. A few hundred frames along it would stop and
> print the error, "Problem loading CRD file." Upon closer examination
> of
> the trajectory I found several exclamation points in the file, always
> appearing just in front of a number. After I removed them the
> trajectory loaded normally into VMD. Does anyone have any idea why
> these exclamation points would appear or what they might mean?

I honestly have no idea how you could get such characters in your trajectory
file. There is certainly nothing in the code that would print this. It is
possible to get *'s in the trajectory file if the coordinates become too
large but in your case this is not what is happening. The fact that removing
them makes it work is amazing. I would have suggested that what you had was
file corruption, this can happen sometimes due to disk / network errors etc
but normally this results in a whole block just being garbage.

Thus in conclusion I have no idea how the !'s would have got there except if
someone somehow edited the file and added them for some strange reason.

Sorry I can't be of any more help. If you can find a way to reliably
reproduce the problem please post it and then we can look into how it
happens.

All the best
Ross

/\
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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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